pik-piam · pascal-sauer · May 13, 2024 · Apr 25, 2024 · May 3, 2024 · May 7, 2024
diff --git a/.buildlibrary b/.buildlibrary
@@ -1,8 +1,10 @@
-ValidationKey: '11333779'
+ValidationKey: '11715040'
 AcceptedWarnings:
 - 'Warning: package ''.*'' was built under R version'
 - 'Warning: namespace ''.*'' is not available and has been replaced'
-AcceptedNotes: unable to verify current time
+AcceptedNotes:
+- unable to verify current time
+- Depends: includes the non-default packages
 AutocreateReadme: yes
 allowLinterWarnings: no
 enforceVersionUpdate: no
diff --git a/CITATION.cff b/CITATION.cff
@@ -2,8 +2,8 @@ cff-version: 1.2.0
 message: If you use this software, please cite it using the metadata from this file.
 type: software
 title: 'mrland: MadRaT land data package'
-version: 0.57.1
-date-released: '2024-05-06'
+version: 0.59.0
+date-released: '2024-05-13'
 abstract: The package provides land related data via the madrat framework.
 authors:
 - family-names: Dietrich
@@ -37,6 +37,8 @@ authors:
   given-names: Felicitas
 - family-names: Hoetten
   given-names: David
+- family-names: Sauer
+  given-names: Pascal
 license: LGPL-3.0
 repository-code: https://github.com/pik-piam/mrland
 doi: 10.5281/zenodo.3822083

diff --git a/DESCRIPTION b/DESCRIPTION
@@ -1,8 +1,8 @@
 Type: Package
 Package: mrland
 Title: MadRaT land data package
-Version: 0.57.1
-Date: 2024-05-06
+Version: 0.59.0
+Date: 2024-05-13
 Authors@R: c(
     person("Jan Philipp", "Dietrich", , "dietrich@pik-potsdam.de", role = c("aut", "cre")),
     person("Abhijeet", "Mishra", role = "aut"),
@@ -18,7 +18,8 @@ Authors@R: c(
     person("Patrick", "von Jeetze", role = "aut"),
     person("Stephen", "Wirth", role = "aut"),
     person("Felicitas", "Beier", role = "aut"),
-    person("David", "Hoetten", role = "aut")
+    person("David", "Hoetten", role = "aut"),
+    person("Pascal", "Sauer", role = "aut")
   )
 Description: The package provides land related data via the madrat
     framework.
@@ -27,24 +28,25 @@ URL: https://github.com/pik-piam/mrland,
     https://doi.org/10.5281/zenodo.3822083
 BugReports: https://github.com/pik-piam/mrland/issues
 Depends:
-    R (>= 2.10.0),
     madrat (>= 1.30),
     magclass (>= 6.13.1),
-    mrdrivers (>= 1.0.0),
-    mrcommons (>= 1.37.0),
-    mrfactors
+    mrcommons (>= 1.41.0),
+    mrfactors (>= 0.4.0),
+    mrfaocore (>= 1.0.0),
+    mrlandcore (>= 1.0.0),
+    R (>= 2.10.0)
 Imports:
-    GDPuc,
-    SPEI,
     countrycode,
     data.table,
     dplyr,
+    GDPuc,
     magpiesets,
-    mstools,
+    mstools (>= 0.6.0),
     ncdf4,
     raster,
     readxl,
     reshape2,
+    SPEI,
     stringr,
     terra,
     withr

diff --git a/NAMESPACE b/NAMESPACE
@@ -25,8 +25,9 @@ import(countrycode)
 import(madrat)
 import(magclass)
 import(mrcommons)
-import(mrdrivers)
 import(mrfactors)
+import(mrfaocore)
+import(mrlandcore)
 import(readxl)
 import(utils)
 importFrom(GDPuc,convertGDP)
@@ -87,14 +88,16 @@ importFrom(magclass,unwrap)
 importFrom(magclass,where)
 importFrom(magpiesets,addLocation)
 importFrom(magpiesets,findset)
-importFrom(mrcommons,toolAggregateCell2Country)
-importFrom(mrcommons,toolCoord2Isocell)
-importFrom(mrcommons,toolGetMappingCoord2Country)
-importFrom(mrcommons,toolHarmonize2Baseline)
-importFrom(mrcommons,toolHoldConstantBeyondEnd)
-importFrom(mrcommons,toolLPJmLVersion)
-importFrom(mrcommons,toolSmooth)
+importFrom(mrlandcore,toolLPJmLVersion)
+importFrom(mstools,toolAggregateCell2Country)
+importFrom(mstools,toolCell2isoCell)
+importFrom(mstools,toolCoord2Isocell)
+importFrom(mstools,toolCountryFillBilateral)
+importFrom(mstools,toolGetMappingCoord2Country)
+importFrom(mstools,toolHarmonize2Baseline)
 importFrom(mstools,toolHoldConstant)
+importFrom(mstools,toolHoldConstantBeyondEnd)
+importFrom(mstools,toolSmooth)
 importFrom(ncdf4,nc_open)
 importFrom(raster,aggregate)
 importFrom(raster,brick)

diff --git a/R/SOMexogenous.R b/R/SOMexogenous.R
@@ -1,34 +1,33 @@
 #' @title calcSOMexogenous
-#' @description 
+#' @description
 #' Uses an exogenous trajectory of Soil organic matter loss nitrogen release
 #' @return List of magpie objects with results on country level, weight on country level, unit and description.
-#' 
+#'
 #' @author Benjamin Leon Bodirsky
 #' @seealso \code{\link{calcOutput}}
 #' @examples
-#' 
-#' \dontrun{ 
+#' \dontrun{
 #' calcOutput("SOMexogenous")
 #' }
 #' @export
-#' @importFrom mrcommons toolHoldConstantBeyondEnd
+#' @importFrom mstools toolHoldConstantBeyondEnd
 #' @importFrom magpiesets findset
 
-calcSOMexogenous <- function(){
-  
-  input <- calcOutput("SOMlossN",cellular=FALSE,aggregate = F)
+calcSOMexogenous <- function() {
+
+  input <- calcOutput("SOMlossN", cellular = FALSE, aggregate = FALSE)
   constant <- toolHoldConstantBeyondEnd(collapseNames(input))
-  getNames(constant)="constant"
-  fadeout_2050 = constant
-  fadeout_2050 = convergence(origin = constant,aim = 0,start_year = "y2020",end_year = "y2050", type="linear")
-  getNames(fadeout_2050)="fadeout_2050"
-  x <- mbind(constant,fadeout_2050)
-  
-  x <- x[,findset("time"),]
-  
-  return(list(x=x,
-              weight=NULL,
-              unit="Tg Nr/yr",
-              description="Nr release through soil organic matter loss")
+  getNames(constant) <- "constant"
+  fadeout2050 <- constant
+  fadeout2050 <- convergence(origin = constant, aim = 0, start_year = "y2020", end_year = "y2050", type = "linear")
+  getNames(fadeout2050) <- "fadeout_2050"
+  x <- mbind(constant, fadeout2050)
+
+  x <- x[, findset("time"), ]
+
+  return(list(x = x,
+              weight = NULL,
+              unit = "Tg Nr/yr",
+              description = "Nr release through soil organic matter loss")
   )
 }
diff --git a/R/calcAvlCropland.R b/R/calcAvlCropland.R
@@ -44,7 +44,7 @@
 #' @importFrom madrat readSource calcOutput
 #' @importFrom magclass dimSums getCells getYears getNames mbind collapseDim as.magpie
 #' @importFrom magpiesets addLocation
-#' @importFrom mrcommons toolCoord2Isocell toolAggregateCell2Country
+#' @importFrom mstools toolCoord2Isocell toolAggregateCell2Country
 #'
 
 calcAvlCropland <- function(marginal_land = "magpie", cell_upper_bound = 0.9, country_level = FALSE, # nolint

diff --git a/R/calcBHIFL.R b/R/calcBHIFL.R
@@ -21,11 +21,10 @@
 #'
 #' @importFrom magpiesets findset addLocation
 #' @importFrom magclass collapseDim
-#' @importFrom mrcommons toolCoord2Isocell
+#' @importFrom mstools toolCoord2Isocell
 #'
 
 calcBHIFL <- function(cells = "lpjcell", nclasses = "seven") {
-
   # Land area (in Mha):
   iniLU <- calcOutput("LanduseInitialisation",
     cellular = TRUE, cells = cells,
@@ -86,7 +85,7 @@ calcBHIFL <- function(cells = "lpjcell", nclasses = "seven") {
 
   # Conservation potential after 2020
   consvPot <- landArea - dimSums(wdpaBase[, "y2020", ], dim = 3) -
-                setCells(urbanLand[, "y2020", "SSP2"], getCells(wdpaBase))
+    setCells(urbanLand[, "y2020", "SSP2"], getCells(wdpaBase))
   consvPot <- toolConditionalReplace(consvPot, "<0", 0)
 
   # Where conservation priority area is larger than conservation potential
@@ -100,7 +99,7 @@ calcBHIFL <- function(cells = "lpjcell", nclasses = "seven") {
   if (nclasses == "seven") {
     # calulate share of respective natveg classes
     natvegShr <- iniLU[, , c("primforest", "secdforest", "other")] /
-                   dimSums(iniLU[, , c("primforest", "secdforest", "other")], dim = 3)
+      dimSums(iniLU[, , c("primforest", "secdforest", "other")], dim = 3)
     natvegShr <- toolConditionalReplace(natvegShr, "is.na()", 0)
 
     # magpie object containing all land classes and their conservation land shares
@@ -113,7 +112,7 @@ calcBHIFL <- function(cells = "lpjcell", nclasses = "seven") {
   } else if (nclasses == "nine") {
     # calulate share of respective natveg classes
     natvegShr <- iniLU[, , c("primforest", "secdforest", "primother", "secdother")] /
-                   dimSums(iniLU[, , c("primforest", "secdforest", "primother", "secdother")], dim = 3)
+      dimSums(iniLU[, , c("primforest", "secdforest", "primother", "secdother")], dim = 3)
     natvegShr <- toolConditionalReplace(natvegShr, "is.na()", 0)
 
     # magpie object containing all land classes and their conservation land shares

diff --git a/R/calcBrooks2005OldConservationPrios.R b/R/calcBrooks2005OldConservationPrios.R
@@ -21,11 +21,10 @@
 #'
 #' @importFrom magpiesets findset addLocation
 #' @importFrom magclass collapseDim
-#' @importFrom mrcommons toolCoord2Isocell
+#' @importFrom mstools toolCoord2Isocell
 #'
 
 calcBrooks2005OldConservationPrios <- function(cells = "lpjcell", nclasses = "seven") {
-
   # Land area (in Mha):
   iniLU <- calcOutput("LanduseInitialisation",
     cellular = TRUE, cells = cells,
@@ -99,7 +98,7 @@ calcBrooks2005OldConservationPrios <- function(cells = "lpjcell", nclasses = "se
 
   # Conservation potential after 2020
   consvPot <- landArea - dimSums(wdpaBase[, "y2020", ], dim = 3) -
-                setCells(urbanLand[, "y2020", "SSP2"], getCells(wdpaBase))
+    setCells(urbanLand[, "y2020", "SSP2"], getCells(wdpaBase))
   consvPot <- toolConditionalReplace(consvPot, "<0", 0)
 
   # Where conservation priority area is larger than conservation potential
@@ -113,7 +112,7 @@ calcBrooks2005OldConservationPrios <- function(cells = "lpjcell", nclasses = "se
   if (nclasses == "seven") {
     # calulate share of respective natveg classes
     natvegShr <- iniLU[, , c("primforest", "secdforest", "other")] /
-                   dimSums(iniLU[, , c("primforest", "secdforest", "other")], dim = 3)
+      dimSums(iniLU[, , c("primforest", "secdforest", "other")], dim = 3)
     natvegShr <- toolConditionalReplace(natvegShr, "is.na()", 0)
 
     # magpie object containing all land classes and their conservation land shares
@@ -126,7 +125,7 @@ calcBrooks2005OldConservationPrios <- function(cells = "lpjcell", nclasses = "se
   } else if (nclasses == "nine") {
     # calulate share of respective natveg classes
     natvegShr <- iniLU[, , c("primforest", "secdforest", "primother", "secdother")] /
-                   dimSums(iniLU[, , c("primforest", "secdforest", "primother", "secdother")], dim = 3)
+      dimSums(iniLU[, , c("primforest", "secdforest", "primother", "secdother")], dim = 3)
     natvegShr <- toolConditionalReplace(natvegShr, "is.na()", 0)
 
     # magpie object containing all land classes and their conservation land shares

diff --git a/R/calcConservationPriorities.R b/R/calcConservationPriorities.R
@@ -28,11 +28,10 @@
 #'
 #' @importFrom magpiesets findset addLocation
 #' @importFrom magclass collapseDim
-#' @importFrom mrcommons toolCoord2Isocell
+#' @importFrom mstools toolCoord2Isocell
 #'
 
 calcConservationPriorities <- function(consvBaseYear = "y1750", cells = "lpjcell", nclasses = "seven") {
-
   # ===============================
   # Get conservation templates
   # ===============================
@@ -270,8 +269,8 @@ calcConservationPriorities <- function(consvBaseYear = "y1750", cells = "lpjcell
               weight = NULL,
               unit = "Mha",
               description = paste0("Land conservation priority targets in each land type. ",
-                                  "Land use in conservation priority areas is based on the ",
-                                  "reference year ", consvBaseYear,
-                                  ifelse(gsub("y", "", consvBaseYear) <= 1800, " (pre-industrial)", "")),
+                                   "Land use in conservation priority areas is based on the ",
+                                   "reference year ", consvBaseYear,
+                                   ifelse(gsub("y", "", consvBaseYear) <= 1800, " (pre-industrial)", "")),
               isocountries = FALSE))
 }
diff --git a/R/calcCriticalConnectivityAreas.R b/R/calcCriticalConnectivityAreas.R
@@ -27,14 +27,14 @@
 #' calcOutput("calcCriticalConnectivityAreas", aggregate = FALSE)
 #' }
 #'
-#' @importFrom mrcommons toolCoord2Isocell
+#' @importFrom mstools toolCoord2Isocell
 #'
 calcCriticalConnectivityAreas <- function(maginput = TRUE, nclasses = "seven",
                                           cells = "lpjcell", mask = "KBA_GSN") {
   if (mask == "KBA") {
-  cca <- readSource("Brennan2022", subtype = "KBA_masked", convert = "onlycorrect")
+    cca <- readSource("Brennan2022", subtype = "KBA_masked", convert = "onlycorrect")
   } else if (mask == "KBA_GSN") {
-  cca <- readSource("Brennan2022", subtype = "KBA_GSN_masked", convert = "onlycorrect")
+    cca <- readSource("Brennan2022", subtype = "KBA_GSN_masked", convert = "onlycorrect")
   } else {
     stop("Option specified for argument 'mask' does not exist.")
   }
@@ -68,7 +68,6 @@ calcCriticalConnectivityAreas <- function(maginput = TRUE, nclasses = "seven",
     cca[, , "CCA"] <- cca[, , "CCA"] * landMismatch[, , "CCA"]
 
     if (nclasses %in% c("seven", "nine")) {
-
       # differentiate primary and secondary forest based on LUH2v2 data
       totForestLUH <- dimSums(luh2v2[, , c("primf", "secdf")], dim = 3) # nolint
       primforestShr <- luh2v2[, , "primf"] / setNames(totForestLUH + 1e-10, NULL)
@@ -94,7 +93,6 @@ calcCriticalConnectivityAreas <- function(maginput = TRUE, nclasses = "seven",
     }
 
     if (nclasses == "nine") {
-
       # separate pasture into pasture and rangeland
       totGrassLUH <- dimSums(luh2v2[, , c("pastr", "range")], dim = 3) # nolint
       pastShr <- luh2v2[, , "pastr"] / setNames(totGrassLUH + 1e-10, NULL)

diff --git a/R/calcCroplandTreecover.R b/R/calcCroplandTreecover.R
@@ -16,7 +16,7 @@
 #' calcOutput("CroplandTreecover", aggregate = FALSE)
 #' }
 #'
-#' @importFrom mrcommons toolCoord2Isocell
+#' @importFrom mstools toolCoord2Isocell
 #'
 calcCroplandTreecover <- function(maginput = TRUE, cells = "magpiecell") {
   treecover <- readSource("Copernicus", subtype = "CroplandTreecover", convert = "onlycorrect")

diff --git a/R/calcGlobalSafetyNet.R b/R/calcGlobalSafetyNet.R
@@ -24,7 +24,7 @@
 #' calcOutput("calcGlobalSafetyNet", aggregate = FALSE)
 #' }
 #'
-#' @importFrom mrcommons toolCoord2Isocell
+#' @importFrom mstools toolCoord2Isocell
 #'
 calcGlobalSafetyNet <- function(maginput = TRUE, nclasses = "seven", cells = "lpjcell") {
   gsn <- mbind(

diff --git a/R/calcHalfEarth.R b/R/calcHalfEarth.R
@@ -21,11 +21,10 @@
 #'
 #' @importFrom magpiesets findset addLocation
 #' @importFrom magclass collapseDim
-#' @importFrom mrcommons toolCoord2Isocell
+#' @importFrom mstools toolCoord2Isocell
 #'
 
 calcHalfEarth <- function(cells = "lpjcell", nclasses = "seven") {
-
   # Land area (in Mha):
   iniLU <- calcOutput("LanduseInitialisation",
                       cellular = TRUE, cells = cells,
@@ -46,8 +45,8 @@ calcHalfEarth <- function(cells = "lpjcell", nclasses = "seven") {
 
   # get WDPA baseline data (1995 - 2020)
   wdpaBase <- calcOutput("ProtectedAreaBaseline",
-                          aggregate = FALSE, cells = cells,
-                          nclasses = nclasses, magpie_input = TRUE)
+                         aggregate = FALSE, cells = cells,
+                         nclasses = nclasses, magpie_input = TRUE)
 
   # make sure that current WDPA protected areas
   # are not part of conservation priority targets
@@ -60,7 +59,7 @@ calcHalfEarth <- function(cells = "lpjcell", nclasses = "seven") {
 
   # Conservation potential after 2020
   consvPot <- landArea - dimSums(wdpaBase[, "y2020", ], dim = 3) -
-                setCells(urbanLand[, "y2020", "SSP2"], getCells(wdpaBase))
+    setCells(urbanLand[, "y2020", "SSP2"], getCells(wdpaBase))
   consvPot <- toolConditionalReplace(consvPot, "<0", 0)
 
   # Where conservation priority area is larger than conservation potential
@@ -74,7 +73,7 @@ calcHalfEarth <- function(cells = "lpjcell", nclasses = "seven") {
   if (nclasses == "seven") {
     # calulate share of respective natveg classes
     natvegShr <- iniLU[, , c("primforest", "secdforest", "other")] /
-                   dimSums(iniLU[, , c("primforest", "secdforest", "other")], dim = 3)
+      dimSums(iniLU[, , c("primforest", "secdforest", "other")], dim = 3)
     natvegShr <- toolConditionalReplace(natvegShr, "is.na()", 0)
 
     # magpie object containing all land classes and their conservation land shares
@@ -87,7 +86,7 @@ calcHalfEarth <- function(cells = "lpjcell", nclasses = "seven") {
   } else if (nclasses == "nine") {
     # calulate share of respective natveg classes
     natvegShr <- iniLU[, , c("primforest", "secdforest", "primother", "secdother")] /
-                   dimSums(iniLU[, , c("primforest", "secdforest", "primother", "secdother")], dim = 3)
+      dimSums(iniLU[, , c("primforest", "secdforest", "primother", "secdother")], dim = 3)
     natvegShr <- toolConditionalReplace(natvegShr, "is.na()", 0)
 
     # magpie object containing all land classes and their conservation land shares